Mercurial > repos > guerler > spring_map
comparison spring_map.xml @ 0:023800b21a2a draft
"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
author | guerler |
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date | Tue, 23 Mar 2021 13:54:20 +0000 |
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children | 5f5cdcfaa1a9 |
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1 <tool id="spring_map" name="SPRING Map" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> | |
2 <description>with BLAST</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 spring_map.py | |
9 @pdb_source@ | |
10 -l '$list' | |
11 -c '$cross' | |
12 -e $evalue | |
13 -o '$output' | |
14 -g '$log' | |
15 ]]> </command> | |
16 <inputs> | |
17 <expand macro="pdb_source" /> | |
18 <param name="list" type="data" format="tabular" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`." /> | |
19 <param name="cross" type="data" format="tabular" label="Cross Reference (unmapped)" help="Unmapped SPRING PDB Cross Reference as produced by SPRING Cross tool." /> | |
20 <param name="evalue" type="float" value="0.0" min="0.0" max="1.0" label="E-value Threshold" help="Specify an e-Value threshold to filter the alignment results" /> | |
21 <expand macro="logfile" /> | |
22 </inputs> | |
23 <outputs> | |
24 <data format="tabular" name="output" label="SPRING Map Cross Reference" /> | |
25 <data format="txt" name="log" label="SPRING Map Log"> | |
26 <filter>logfile</filter> | |
27 </data> | |
28 </outputs> | |
29 <tests> | |
30 <test expect_num_outputs="1"> | |
31 <conditional name="pdb_source"> | |
32 <param name="pdb_source_selector" value="history" /> | |
33 <param name="ffdata" value="cross/pdb.ffdata" /> | |
34 <param name="ffindex" value="cross/pdb.ffindex" /> | |
35 </conditional> | |
36 <param name="list" value="map/chains.tabular" ftype="tabular" /> | |
37 <param name="cross" value="cross/reference.tabular" ftype="tabular" /> | |
38 <output name="output" file="map/mapped.reference.tabular" /> | |
39 </test> | |
40 <test expect_num_outputs="2"> | |
41 <conditional name="pdb_source"> | |
42 <param name="pdb_source_selector" value="indexed" /> | |
43 <param name="pdb" value="pdb01_cross" /> | |
44 </conditional> | |
45 <param name="list" value="map/chains.tabular" ftype="tabular" /> | |
46 <param name="cross" value="cross/reference.tabular" ftype="tabular" /> | |
47 <param name="logfile" value="true" /> | |
48 <output name="output" file="map/mapped.reference.tabular" /> | |
49 </test> | |
50 </tests> | |
51 <help><![CDATA[ | |
52 | |
53 **What it does** | |
54 | |
55 Creates additional columns for the SPRING cross reference containing the chain identifier of the homologues from the template library. | |
56 | |
57 ]]> </help> | |
58 <expand macro="citations" /> | |
59 </tool> |